Neon Genesis Evangelion: The Spirit in the Machine
by Kuro Majiyo
Summary: We know the tale of Shinji, his struggles, his pain. However, sometimes, there is something different. Sometimes, a spirit will fight on, even after death. Sometimes, a coward can be a hero, when watched over by a legend.
1. Prologue

Prologue

Kamina looked on, as his brother and team Dai-Gurren went off towards their final battle. He had finished his job, it was now in their hands. Kamina smirked. "Brother, remember to believe in yourself." he thought as he watched the distant green streak pass out of the sky. The Dimensional Corridor collapsed when it's prisoners left, surrounding Kamina with blackness. He closed his eyes, and sighed. Existing had been fun while it lasted.

Universes apart, and a young boy thinks similar words. Screaming for his life, he sits next to a lady a few year older then him as a gigantic being follows them, slicing through the numerous helicopters attempting to slow it's progress into Tokyo-3. His name: Shinji Ikari, son of NERV head Gendo Ikari. He had been summoned to see his father for the first time in years. He looked over as the driver screamed. "OH SHIT!!! Their using an N2 mine. GET UNDER ME KID!" He complied, and there was a huge blast. Light filled the sky.


	2. Chapter 1: I Mustn't Run Away

**Chapter 1**

_I Mustn't Run Away_

Shinji looked up at his father. It had been years since he had seen the cold man's face. He looked at him, and felt all the emotions, all the turmoil of not knowing why. Why had he been left with his aunt and uncle, why had his father not seen him in years? Why? Why? Why? "Why Father? Why have you called me here?" He shouted right at the dispassionate man who was genetically related to him.

"Exactly why you think, boy." replied Gendo. The man was taller then Shinji, but his eyes were dead, cold, while the rest of his features were similar, a thin beard growing on his chin. A calculating man.

Shinji's eyes widened in fear. A realization came to him. "You wish me to pilot that robot, against the monster outside?" The father nodded. "No. No. You haven't seen me in years, and you call me here so I can die for you." He collapsed to his knees. "Why father? Why now? WHY ME?!?" he started crying.

Gendo's face curled into a disgusted snarl for a fraction of a second, before returning to the cold implacable look that most who had seen NERV's head were accustomed to. "Because others can't. Because you have become useful to me."

Shinji simply continued crying. He couldn't do it. He couldn't do it. He _couldn't_ do it. "I can't do it! I have no clue how to fight, let alone use a robot. How can you expect me to?"

Gendo looked down upon his offspring, pitilessly. "Either do it or leave." and with that, he rose his phone to his face. "Bring Rei to Evangelion Unit One."

"_Can she fight?" _said the voice on the other end of the comm system.

Gendo replied. "She is still breathing, isn't she?" With those words, Gendo condemned his puppet to death, unless the useless shell in front of him, his _offspring_, would do as he was told. No matter, she could be replaced. Around him, others scrambled to set up the Evangelion for the wounded pilot, Rei Ayanami. Gendo walked away, walked away from the room where stood the coward who was of his blood.

Shinji on the other hand, was deep inside himself, searing with pain. His father didn't need him after all. This was just a game, another way of hurting him. _Father. Why_? Then, Shinji looked over, as the door opened, revealing a girl on a stretcher, barely conscious. _This is who they were sending in my place?_ Shinji cried even further. _Coward Coward Coward._ He was a coward, too scared to go instead of this injured girl.

The entire room rocked, and some of the ceiling tore off, a hundred pounds of concrete falling towards the walkway where Shinji and the wounded girl stood. "WATCH OUT!" cried Shinji, leaping towards the wounded girl and attempting to push her out of the way. He expected oblivion to follow, and was quite surprised when he looked up. A giant hand, the Evangelion's, had caught the debris.

"The Eva moved! How did that happen?" said one of the lab techs. Another nodded in agreement. There was no precedent to this.

Doctor Ristuko was noticeably distressed. "That is NOT possible. The entry plug hasn't been inserted yet, how could it have moved?"

Her colleague, Misato, posed her theory. "Perhaps it's protecting him. The Evangelion might already be syncing with Shinji, even without the entry plug." Both women winced at the thought. It meant another week without sleep later, but for now there was no time to worry about such things.

As the two scientist reeled at the possibilities, Shinji ran over to the other pilot. "I mustn't run away. I mustn't run away. I mustn't run away." This mantra echoed throughout him, and then he reached for Rei, and took her shoulders by his hand. The girl was approximately his age, slightly taller, with blue hair and red eyes, one covered by a bandage. There was nothing in the eye he could see. It was glassed over, seeing but unseeing. For a second Shinji thought that the girl was dead, but he felt her heart beat. She was barely conscious, and yet they wished her to fight. For a second, Shinji's fear was outweighed by his outrage. He looked up. "I'll do it. I'll pilot it."


End file.
